diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 369 |
1 files changed, 364 insertions, 5 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 229fd34d2a..3ddb91714a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -106,6 +106,7 @@ #:use-module (gnu packages java-compression) #:use-module (gnu packages jemalloc) #:use-module (gnu packages jupyter) + #:use-module (gnu packages libffi) #:use-module (gnu packages linux) #:use-module (gnu packages logging) #:use-module (gnu packages lsof) @@ -1216,14 +1217,14 @@ sequencing.") (define-public python-biopython (package (name "python-biopython") - (version "1.73") + (version "1.76") (source (origin (method url-fetch) ;; use PyPi rather than biopython.org to ease updating (uri (pypi-uri "biopython" version)) (sha256 (base32 - "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh")))) + "0wlch9xpa0fpgjzyxi6jsfca6iakaq9a05927xg8vqnmvaccnwrq")))) (build-system python-build-system) (arguments `(#:phases @@ -1244,6 +1245,18 @@ dealing with alignments; code making it easy to split up parallelizable tasks into separate processes; and more.") (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE")))) +(define-public python-biopython-1.73 + (package + (inherit python-biopython) + (version "1.73") + (source (origin + (method url-fetch) + ;; use PyPi rather than biopython.org to ease updating + (uri (pypi-uri "biopython" version)) + (sha256 + (base32 + "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh")))))) + (define-public python2-biopython (package-with-python2 python-biopython)) @@ -1270,6 +1283,133 @@ relying on a complex dependency tree.") (define-public python2-fastalite (package-with-python2 python-fastalite)) +(define-public ciri-long + (package + (name "ciri-long") + (version "1.0.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bioinfo-biols/CIRI-long") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10k88i1fcqchrrjv82rmylwvbwqfba0n51palhig9hsg71xs0dbi")) + ;; Delete bundled binary + (snippet '(delete-file "libs/ccs")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "setup.py" + (("'argparse[^']*',") "") ; only for python2 + (("==") ">=")))) + (add-before 'build 'build-libssw + (lambda _ + (with-directory-excursion "libs/striped_smith_waterman" + (invoke "make" "libssw.so"))))))) + (inputs + `(("python-biopython" ,python-biopython) + ("python-bwapy" ,python-bwapy) + ("python-cython" ,python-cython) + ("python-levenshtein" ,python-levenshtein) + ("python-mappy" ,python-mappy) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-pysam" ,python-pysam) + ("python-pyspoa" ,python-pyspoa) + ("python-scikit-learn" ,python-scikit-learn) + ("python-scipy" ,python-scipy))) + (native-inputs + `(("python-nose" ,python-nose) + ("python-setuptools" ,python-setuptools))) + (home-page "https://ciri-cookbook.readthedocs.io/") + (synopsis "Circular RNA identification for Nanopore sequencing") + (description "CIRI-long is a package for circular RNA identification using +long-read sequencing data.") + (license license:expat))) + +(define-public qtltools + (package + (name "qtltools") + (version "1.3.1") + (source (origin + (method url-fetch/tarbomb) + (uri (string-append "https://qtltools.github.io/qtltools/" + "binaries/QTLtools_" version + "_source.tar.gz")) + (sha256 + (base32 + "13gdry5l43abn3464fmk8qzrxgxnxah2612r66p9dzhhl92j30cd")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no tests included + #:make-flags + (list (string-append "BOOST_INC=" + (assoc-ref %build-inputs "boost") "/include") + (string-append "BOOST_LIB=" + (assoc-ref %build-inputs "boost") "/lib") + (string-append "HTSLD_INC=" + (assoc-ref %build-inputs "htslib") "/include") + (string-append "HTSLD_LIB=" + (assoc-ref %build-inputs "htslib") "/lib") + (string-append "RMATH_INC=" + (assoc-ref %build-inputs "rmath-standalone") + "/include") + (string-append "RMATH_LIB=" + (assoc-ref %build-inputs "rmath-standalone") + "/lib")) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-linkage + (lambda _ + (substitute* "qtltools/Makefile" + (("libboost_iostreams.a") + "libboost_iostreams.so") + (("libboost_program_options.a") + "libboost_program_options.so") + (("-lblas") "-lopenblas")))) + (add-before 'build 'chdir + (lambda _ (chdir "qtltools"))) + (replace 'configure + (lambda _ + (substitute* "qtltools/Makefile" + (("LIB_FLAGS=-lz") + "LIB_FLAGS=-lz -lcrypto -lssl") + (("LIB_FILES=\\$\\(RMATH_LIB\\)/libRmath.a \ +\\$\\(HTSLD_LIB\\)/libhts.a \ +\\$\\(BOOST_LIB\\)/libboost_iostreams.a \ +\\$\\(BOOST_LIB\\)/libboost_program_options.a") + "LIB_FILES=$(RMATH_LIB)/libRmath.so \ +$(HTSLD_LIB)/libhts.so \ +$(BOOST_LIB)/libboost_iostreams.so \ +$(BOOST_LIB)/libboost_program_options.so")))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (mkdir-p bin) + (install-file "bin/QTLtools" bin))))))) + (inputs + `(("curl" ,curl) + ("gsl" ,gsl) + ("boost" ,boost) + ("rmath-standalone" ,rmath-standalone) + ("htslib" ,htslib-1.3) + ("openssl" ,openssl) + ("openblas" ,openblas) + ("zlib" ,zlib))) + (home-page "https://qtltools.github.io/qtltools/") + (synopsis "Tool set for molecular QTL discovery and analysis") + (description "QTLtools is a tool set for molecular QTL discovery +and analysis. It allows to go from the raw genetic sequence data to +collection of molecular @dfn{Quantitative Trait Loci} (QTLs) in few +easy-to-perform steps.") + (license license:gpl3+))) + (define-public bpp-core ;; The last release was in 2014 and the recommended way to install from source ;; is to clone the git repository, so we do this. @@ -7448,6 +7588,33 @@ clustering analysis, differential analysis, motif inference and exploration of single cell ATAC-seq sequencing data.") (license license:gpl3))) +(define-public r-umi4cpackage + (let ((commit "88b07d896a137418ba6c31c2474b9dbe1d86fc20") + (revision "1")) + (package + (name "r-umi4cpackage") + (version (git-version "0.0.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tanaylab/umi4cpackage") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0bjzamdw2lcfhlbzc0vdva87c3wwnij8jsvnrpx4wyyxvpcz13m5")))) + (properties `((upstream-name . "umi4cPackage"))) + (build-system r-build-system) + (propagated-inputs + `(("r-misha" ,r-misha) + ("r-zoo" ,r-zoo))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/tanaylab/umi4cpackage") + (synopsis "Processing and analysis of UMI-4C contact profiles.") + (description "This is a package that lets you process UMI-4C data from +scratch to produce nice plots.") + (license license:expat)))) + (define-public r-shinycell (let ((commit "aecbd56e66802f28e397f5ae1f19403aadd12163") @@ -7576,6 +7743,86 @@ of transcriptional heterogeneity among single cells.") ;; See https://github.com/hms-dbmi/scde/issues/38 (license license:gpl2))) +(define-public r-misha + (package + (name "r-misha") + (version "4.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tanaylab/misha") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0bgivx3lzjh3173jsfrhb5kvhjsn53br0n4hmyx7i3dwy2cnnp2p")) + ;; Delete bundled executable. + (snippet + '(delete-file "exec/bigWigToWig")))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'do-not-use-bundled-bigWigToWig + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "R/misha.R" + (("get\\(\".GLIBDIR\"\\), \"/exec/bigWigToWig") + (string-append "\"" + (assoc-ref inputs "kentutils") + "/bin/bigWigToWig")))))))) + (inputs + `(("kentutils" ,kentutils))) + (home-page "https://github.com/tanaylab/misha") + (synopsis "Toolkit for analysis of genomic data") + (description "This package is intended to help users to efficiently +analyze genomic data resulting from various experiments.") + (license license:gpl2))) + +(define-public r-shaman + (let ((commit "d6944e8ac7bd1dbd5c6cec646eafc1d19d0ca96f") + (release "2.0") + (revision "2")) + (package + (name "r-shaman") + (version (git-version release revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tanaylab/shaman") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "03sx138dzpfiq23j49z0m0s4j79855mrg64hpj9c83408wzphxi6")) + (snippet + ;; This file will be generated. + '(delete-file "inst/doc/shaman-package.R")))) + (build-system r-build-system) + (propagated-inputs + `(("r-data-table" ,r-data-table) + ("r-domc" ,r-domc) + ("r-ggplot2" ,r-ggplot2) + ("r-gviz" ,r-gviz) + ("r-misha" ,r-misha) + ("r-plyr" ,r-plyr) + ("r-rann" ,r-rann) + ("r-rcpp" ,r-rcpp) + ("r-reshape2" ,r-reshape2) + ;; For vignettes + ("r-rmarkdown" ,r-rmarkdown) + ("r-knitr" ,r-knitr))) + (home-page "https://github.com/tanaylab/shaman") + (synopsis "Sampling HiC contact matrices for a-parametric normalization") + (description "The Shaman package implements functions for +resampling Hi-C matrices in order to generate expected contact +distributions given constraints on marginal coverage and +contact-distance probability distributions. The package also provides +support for visualizing normalized matrices and statistical analysis +of contact distributions around selected landmarks.") + ;; Any version of the GPL + (license license:gpl3+)))) + (define-public r-centipede (package (name "r-centipede") @@ -7639,6 +7886,46 @@ includes software to ") (license license:cc0)))) +(define-public gdc-client + (package + (name "gdc-client") + (version "1.6.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/NCI-GDC/gdc-client.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0cagawlzjwj3wam10lv64xgbfx4zcnzxi5sjpsdhq7rn4z24mzc2")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "requirements.txt" + (("==") ">="))))))) + (inputs + `(("python-cryptography" ,python-cryptography) + ("python-intervaltree" ,python-intervaltree) + ("python-jsonschema" ,python-jsonschema) + ("python-lxml" ,python-lxml) + ("python-ndg-httpsclient" ,python-ndg-httpsclient) + ("python-progressbar2" ,python-progressbar2) + ("python-pyasn1" ,python-pyasn1) + ("python-pyopenssl" ,python-pyopenssl) + ("python-pyyaml" ,python-pyyaml) + ("python-requests" ,python-requests) + ("python-termcolor" ,python-termcolor))) + (home-page "https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool") + (synopsis "GDC data transfer tool") + (description "The gdc-client provides several convenience functions over +the GDC API which provides general download/upload via HTTPS.") + (license license:asl2.0))) + (define-public vsearch (package (name "vsearch") @@ -11642,14 +11929,14 @@ set.") (define-public instrain (package (name "instrain") - (version "1.5.2") + (version "1.5.4") (source (origin (method url-fetch) (uri (pypi-uri "inStrain" version)) (sha256 (base32 - "0ykqlpf6yz4caihsaz3ys00cyvlr7wdj4s9a8rh56q5r8xf80ic0")))) + "05w1lw75x4lwkzg4qpi055g7hdjp9rnc4ksbxg2hfgksq9djk0hx")))) (build-system python-build-system) (arguments `(#:phases @@ -11662,7 +11949,7 @@ set.") (("from job_utils") "from .job_utils"))))))) (inputs - `(("python-biopython" ,python-biopython) + `(("python-biopython" ,python-biopython-1.73) ("python-boto3" ,python-boto3) ("python-h5py" ,python-h5py) ("python-lmfit" ,python-lmfit) @@ -14995,6 +15282,78 @@ line, interactively explore genomic data within Jupyter environment or web browser.") (license license:gpl3+))) +(define-public python-pyspoa + (package + (name "python-pyspoa") + (version "0.0.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/nanoporetech/pyspoa") + (commit (string-append "v" version)) + (recursive? #true))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1lgf2shzhxkcsircd6vy46h27pjljd5q95fyz1cm3lkk702qbnzx")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'build-libspoa + (lambda _ + (mkdir-p "src/build") + (with-directory-excursion "src/build" + (invoke "cmake" + "-Dspoa_optimize_for_portability=ON" + "-DCMAKE_BUILD_TYPE=Release" + "-DCMAKE_CXX_FLAGS=\"-I ../vendor/cereal/include/\" -fPIC" + "..") + (invoke "make")))) + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "python" "tests/test_pyspoa.py"))))))) + (propagated-inputs + `(("pybind11" ,pybind11))) + (native-inputs + `(("cmake" ,cmake-minimal))) + (home-page "https://github.com/nanoporetech/pyspoa") + (synopsis "Python bindings for the SIMD partial order alignment library ") + (description + "This package provides Python bindings for spoa, a C++ implementation of +the @dfn{partial order alignment} (POA) algorithm (as described in +10.1093/bioinformatics/18.3.452) which is used to generate consensus +sequences") + (license license:expat))) + +(define-public python-bwapy + (package + (name "python-bwapy") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "bwapy" version)) + (sha256 + (base32 "090qwx3vl729zn3a7sksbviyg04kc71gpbm3nd8dalqp673x1npw")))) + (build-system python-build-system) + (propagated-inputs + `(("python-cffi" ,python-cffi) + ("python-setuptools" ,python-setuptools) + ("python-wheel" ,python-wheel))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/ACEnglish/bwapy") + (synopsis "Python bindings to bwa alinger") + (description "This package provides Python bindings to the bwa mem +aligner.") + ;; These Python bindings are licensed under Mozilla Public License 2.0, + ;; bwa itself is licenced under GNU General Public License v3.0. + (license license:mpl2.0))) + (define-public scregseg (package (name "scregseg") |